3D tomographic reconstruction of high contrast objects such as contrast agent enhanced blood vessels or bones from x-ray images acquired by isocentric C-arm systems recently gained interest. For tomographic reconstruction, a sequence of images is captured during the C-arm rotation around the patient and the precise projection geometry has to be determined for each image. This is a difficult task, as C- arms usually do not provide accurate information about their projection geometry. Standard methods propose the use of an x-ray calibration phantom and an offline calibration, when the motion of the C-arm is supposed to be reproducible between calibration and patient run. However, mobile C-arms usually do not have this desirable property. Therefore, an online recovery of projection geometry is necessary. Here, we study the use of external tracking systems such as Polaris or Optotrak from Northern Digital, Inc., for online calibration. In order to use the external tracking system for recovery of x-ray projection geometry two unknown transformations have to be estimated. We describe our attempt to solve this calibration problem. These are the relations between x-ray imaging system and marker plate of the tracking system as well as worked and sensor coordinate system. Experimental result son anatomical data are presented and visually compared with the results of estimating the projection geometry with an x-ray calibration phantom.